The healthcare IoT system is considered to be a significant and modern medical system. There is broad consensus that these systems will play a vital role in the achievement of economic growth in numerous growth countries. Among the major challenges preventing the fast and widespread adoption of such systems is the failure to maintain the data privacy of patients and the integrity of remote clinical diagnostics. Recently, the author proposed an end-to-end authentication scheme for healthcare IoT systems (E2EA), to provide a mutual authentication with a high data rate between the communication nodes of the healthcare IoT systems. Although the E2EA authentication scheme supports numerous attractive security services to resist various types of attack, there is an ambiguous view of the impact of the desynchronization attack on the E2EA authentication scheme. In general, the performance of the authentication scheme is considered a critical issue when evaluating the applicability of such schemes, along with the security services that can be achieved. Therefore, this paper discusses how the E2EA authentication scheme can resist the desynchronization attack through all possible attack scenarios. Additionally, the effect of the desynchronization attack on the E2EA scheme performance is analyzed in terms of its computation and communication costs, based on a comparison with the recently related authentication schemes that can prevent such attack. Moreover, this research paper finds that the E2EA authentication scheme can not only prevent the desynchronization attack, but also offers a low cost in terms of computations and communications, and can maintain consistency and synchronization between the communication nodes of the healthcare IoT systems during the next authentication sessions.